basil 0.0.3 → 0.0.4
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- data/basil.gemspec +1 -1
- data/lib/basil.rb +1 -3
- data/lib/basil/cli.rb +2 -1
- data/readme.md +5 -3
- metadata +4 -5
- data/lib/basil/version.rb +0 -3
data/basil.gemspec
CHANGED
data/lib/basil.rb
CHANGED
data/lib/basil/cli.rb
CHANGED
@@ -20,6 +20,7 @@ module Basil
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20
20
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handles << reads_handle
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21
21
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records_format = records.format
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22
22
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pretrim = opts[:pretrim] || 0
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23
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+
afttrim = -1*opts[:afttrim] || -1
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23
24
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end
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24
25
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25
26
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if File.exist? out_dir
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@@ -39,7 +40,7 @@ module Basil
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39
40
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trimmed_sequence = record.sequence
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40
41
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end
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41
42
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42
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-
trimmed_sequence = record.sequence[pretrim
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43
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+
trimmed_sequence = record.sequence[pretrim..afttrim]
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43
44
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44
45
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new_record = Fasta.new :name => record.name, :sequence => trimmed_sequence
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45
46
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buffer.add_to File.join(out_dir, barcode + ".#{records_format}"), new_record
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data/readme.md
CHANGED
@@ -4,13 +4,16 @@ Yet another tool for splitting barcoded sequences. It had to be done.
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4
4
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5
5
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## Installation
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6
6
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7
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+
You're gonna need Ruby 1.8.7 or better.
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8
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+
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7
9
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(sudo) gem install basil
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8
10
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9
11
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## Features
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12
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11
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-
-
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13
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+
**Demultiplexes multiplexed high-throughput sequencing data for Illumina, Roche 454, IonTorrent, _etc_... sequence data in their native formats**
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14
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+
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12
15
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- Supports unlimited number of barcodes
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13
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-
- Trimming from left
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16
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+
- Trimming from left end of read
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14
17
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- Barcodes provided as simple .csv file
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15
18
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- Support input filetypes:
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16
19
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- Fastq
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@@ -19,7 +22,6 @@ Yet another tool for splitting barcoded sequences. It had to be done.
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19
22
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## TODO
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20
23
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|
21
24
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- Support regexp in barcodes input.
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22
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-
- QSEQ (Illumina)
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23
25
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|
24
26
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## Usage
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25
27
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metadata
CHANGED
@@ -1,13 +1,13 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: basil
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
hash:
|
4
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+
hash: 23
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5
5
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prerelease:
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6
6
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segments:
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7
7
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- 0
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8
8
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- 0
|
9
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-
-
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10
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-
version: 0.0.
|
9
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+
- 4
|
10
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+
version: 0.0.4
|
11
11
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platform: ruby
|
12
12
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authors:
|
13
13
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- Austin G. Davis-Richardson
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@@ -15,7 +15,7 @@ autorequire:
|
|
15
15
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bindir: bin
|
16
16
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cert_chain: []
|
17
17
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|
18
|
-
date: 2012-05-
|
18
|
+
date: 2012-05-15 00:00:00 Z
|
19
19
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dependencies:
|
20
20
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- !ruby/object:Gem::Dependency
|
21
21
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name: dna
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@@ -95,7 +95,6 @@ files:
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95
95
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- lib/basil/basil.rb
|
96
96
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- lib/basil/buffer.rb
|
97
97
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- lib/basil/cli.rb
|
98
|
-
- lib/basil/version.rb
|
99
98
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- readme.md
|
100
99
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- spec/basil_spec.rb
|
101
100
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- spec/buffer_spec.rb
|
data/lib/basil/version.rb
DELETED